U.S. District Judge Samuel Conti has refused to overturn the agency’s approval of the crop, which was genetically engineered to withstand glyphosate herbicides.

The biotech trait was developed by the Monsanto Co. and allows farmers to spray glyphosate directly over alfalfa, leaving the crop undamaged while killing weeds.

In his Dec. 5 ruling, Conti repeatedly said that arguments against the crop’s commercialization were unpersuasive and lacked merit.

The USDA’s Animal and Plant Health Inspection Service, or APHIS, took a “hard look” at transgenic alfalfa’s potential effects, as required under federal environmental law, he said.

“None of the purported deficiencies raised by plaintiffs in this area, considered independently or holistically, provide sufficient grounds to set aside APHIS’s deregulation determination,” said Conti.

The Center for Food Safety, which opposed the crop’s deregulation, vowed to challenge the ruling in the 9th U.S. Circuit Court of Appeals.

“We disagree with it and will be appealing,” said George Kimbrell, an attorney for the non-profit group.

The National Alfalfa Alliance sees the ruling as a vindication of USDA’s scientific analysis of Roundup Ready alfalfa, said Beth Nelson, the trade group’s president.

“We were hopeful and confident that the ruling would turn out the way it did,” she said. “The concern in the lawsuit was not a safety concern, it was procedural.”

Demand for the transgenic alfalfa was strong among farmers in 2011, with some estimates pegging market penetration at 50 percent in terms of acreage in the West, said Mark McCaslin, president of Forage Genetics International.

The company is licensed by Monsanto to market Roundup Ready alfalfa seed.

“Demand was brisk. Growers are interested in at least trying the technology,” he said.

McCaslin characterized the ruling as a blow for “grower choice,” and said he was heartened by the support from farmers and farm groups that voluntarily intervened in the case as defendants.

“I don’t think there’s any precedent for that,” he said.

The judge fundamentally sided with USDA’s view of its limited authority over genetically engineered crops — a key point in the case and presumably an important issue on appeal.

During oral arguments in December 2011, the USDA said its “hands were tied” in deciding to deregulate the crop, but biotech critics argued the agency “refused to acknowledge its authority” to restrict it.

Conti agreed with USDA that “once APHIS determined that (Roundup Ready alfalfa) did not pose a plant pest risk, it lacked further discretionary authority to regulate the crop…”

Conti rejected that argument, ruling that “there is no indication that Congress intended APHIS to regulate genetically engineered crops as plant pests based on their potential to interbreed with other crops.”

The complaint said the agency inadequately analyzed the potential for “super weeds,” which plaintiffs said will develop as unwanted plants become resistant to glyphosate herbicides.

Conti disagreed, ruling that nothing in federal plant protection law “suggests that APHIS was required to consider the effects of increased herbicide use or the development of herbicide resistant weeds in making this assessment.”

The impact of Roundup Ready alfalfa on endangered and threatened species was also raised by critics, who claimed that increased glyphosate usage would harm federally protected species.

Endangered Species Act concerns about glyphosate are the domain of the U.S. Environmental Protection Agency, which regulates pesticides, and thus don’t have to be analyzed by USDA as part of the deregulation process, said Conti.

“APHIS has no authority to regulate where and how glyphosate is used,” he said.

The biotech crop was deregulated for the second time a year ago, after USDA completed a court-ordered environmental impact statement that reviewed its potential impacts.

The agency had previously allowed the crop to be cultivated without restriction in 2005 after completing a less comprehensive environmental analysis. However, a federal judge found that assessment was insufficiently thorough and overturned the agency’s approval in 2007.

In 2010, the U.S. Supreme Court upheld the judge’s decision to vacate USDA’s approval of the crop, though it did reverse a farther-reaching injunction the court had also imposed.